Package: eDNAjoint
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
        in a Bayesian Framework
Version: 0.3.3
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Authors@R: 
    c(person("Abigail G.", "Keller", role = c("aut", "cre"), email="agkeller@berkeley.edu"),
    person("Ryan P.", "Kelly", role = "ctb", email="rpkelly@uw.edu"),
    person("Chitra M.", "Saraswati", role = "rev"),
    person("Saras M.", "Windecker", role = "rev"))
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and gear scaling coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
License: GPL-3
URL: https://github.com/ropensci/eDNAjoint,
        https://docs.ropensci.org/eDNAjoint/
BugReports: https://github.com/ropensci/eDNAjoint/issues
Encoding: UTF-8
RoxygenNote: 7.3.2
Biarch: true
Depends: R (>= 4.1)
Imports: bayestestR, dplyr, ggplot2, lifecycle, loo, methods, Rcpp (>=
        0.12.0), RcppParallel (>= 5.0.1), rlist, rstan (>= 2.26.23),
        rstantools (>= 2.3.1.1), tidyr, scales
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.26.23), StanHeaders (>=
        2.26.22)
SystemRequirements: GNU make
LazyData: true
Suggests: bayesplot, knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2025-06-21 00:25:49 UTC; jovyan
Author: Abigail G. Keller [aut, cre],
  Ryan P. Kelly [ctb],
  Chitra M. Saraswati [rev],
  Saras M. Windecker [rev]
Repository: CRAN
Date/Publication: 2025-06-21 02:30:05 UTC
Built: R 4.5.0; aarch64-apple-darwin20; 2025-06-21 04:09:20 UTC; unix
Archs: eDNAjoint.so.dSYM
